[R] paraPen in gam [mgcv 1.4-1.1] and centering constraints

Daniel Sabanés Bové daniel.sabanesbove at campus.lmu.de
Mon Feb 9 22:19:37 CET 2009


thank you very much for your very instructive response!

Your explanation has not only justified my intuitive solution to just
delete the corresponding row & column of the penalty matrix, when
choosing a reference category for dummy coding, but leads to a much
better understanding of this important issue.

Thanks again,

Simon Wood schrieb:
> Daniel, 
> There's nothing built in to constraint the coefficients in this way, but it's 
> not too difficult to reparameterize to impose any linear constraint. The key 
> is to find an orthogonal basis for  null space of the constraint. Then it's 
> easy to re-parameterize to work in that space. Here's a simple linear model 
> based example ....
> ## simulated problem: linear model subject to constraint
> ## i.e y = X b + e subject to C b=0
> X <- matrix(runif(40),10,4) ## a model matrix
> y <- rnorm(10)              ## a response
> C <- matrix(1,1,4)          ## a constraint matrix so C b = 0
> ## Get a basis for null space of constraint...
> qrc <- qr(t(C))             
> Z <- qr.Q(qrc,complete=TRUE)[,(nrow(C)+1):ncol(C)]
> ## absorb constraint into basis...
> XZ <- X%*%Z
> ## fit model....
> b <- lm(y~XZ-1)
> ## back to original parameterization
> beta <- Z%*%coef(b)
> sum(beta) ## it works!
> ## If there had been a penalty matrix, S, as well, 
> ## then it should have been transformed as follows....
> S <- t(Z)%*%S%*%Z
> ... So provided that you have the model matrix for the term that you want to 
> penalize in `gam' then it's just a matter of transforming that model matrix 
> and corresponding penalty/ies, using a null space matrix like Z.
> Note that the explicit formation of Z is not optimally efficient here, but 
> this won't have a noticeable impact on  the total computational cost in this 
> context anyway (given that mgcv is not able to make use of all that lovely 
> sparcity in the MRF, :-( ).
> Hope this helps.
> best,
> Simon 
> On Saturday 07 February 2009 21:00, Daniel Sabanés Bové wrote:
>> Dear Mr. Simon Wood, dear list members,
>> I am trying to fit a similar model with gam from mgcv compared to what I
>> did with BayesX, and have discovered the relatively new possibility of
>> incorporating user-defined matrices for quadratic penalties on
>> parametric terms using the "paraPen" argument. This was really a very
>> good idea!
>> However, I would like to constraint the coefficients belonging to one
>> penalty matrix to sum to zero. So I would like to have the same
>> centering constraint on user-defined penalized coefficient groups like
>> it is implemented for the spline smoothing terms. The reason is that I
>> have actually a factor coding different regions, and the penalty matrix
>> results from the neighborhood structure in a Gaussian Markov Random
>> Field (GMRF). So I can't choose one region as the reference category,
>> because then the structure in the other regions would not contain the
>> same information as before...
>> Is there a way to constraint a group of coefficients to sum to zero?
>> Thanks in advance,
>> Daniel Sabanes

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